Studies regarding the genetic basis of human cancer progression have allowed many advances toward finding effective treatments for this disease. Beyond providing an effective treatment for cancer, genetic analyses can provide other essential information about progression of the disease. Cancer patients in the early stages of the disease, for example, would typically greatly benefit from simply knowing more about the aggressiveness that their cancer is likely to exhibit, how their cancer is likely to progress, whether it is likely to metastasize, whether it is likely to recur after therapy (and how quickly it might recur), and so forth. With this type of knowledge in hand, physicians could respond by applying more aggressive therapies for patients with cancers that will likely exhibit particularly aggressive malignant behavior. Treatments could be properly tailored to the patient based on prognosis for that patient's particular disease state.
Recent studies suggest that more aggressive cancers may have some recognizable and measurable characteristics that distinguish them from the less aggressive types. Studies suggest that some types of cancers include a small number of cells in tumors with significant biological resemblance to stem cells, which are unspecialized, precursor cells with the ability to quickly divide and differentiate to give rise to specific specialized cells (Al-Hajj, M., Wicha, M. S., et al., M. F. Prospective identification of tumorigenic breast cancer cells. Proc. Natl. Acad. Sci. USA 2003, 100:3983-3988; Pardal, R., Clarke, M. F., Morrison, S. J. Applying the principle of stem-cell biology to cancer. Nature Review Cancer 2003, 3:895-902; Smalley, M. and Ashworth, A. Stem cells and breast cancer: a field in transit. Nature Review Cancer 2003, 3:832-844, each incorporated herein by reference). For a pluripotent stem cell-like phenotype, self-renewal ability is an essential defining property distinguishing stem cells from other cell types (Dick, J. E. Self-renewal writ in blood. Nature 2003, 423:231-233, incorporated herein by reference). Similarly, in cancer stem cells, this self-renewal ability can play an important role in tumor development, especially in more aggressive cancers. This small population of cancer stem cells within tumors can allow replication that seeds the growth of additional cancer cells. The presence of a rare stem-cell resembling population of cancer cells among the heterogeneous mix of cells comprising a tumor appears to be essential for sustained tumor growth and may contribute to the emergence of metastatic cancer cells during tumor progression (Pardal, R., Clarke, M. F., Morrison, S. J. Applying the principle of stem-cell biology to cancer. Nature Review Cancer 2003, 3:895-902; Al-Hajj, M., et al., Prospective identification of tumorigenic breast cancer cells. Proc. Natl. Acad. Sci. USA 2003, 100:3983-3988; Smalley, M. and Ashworth, A. Stem cells and breast cancer: a field in transit. Nature Review Cancer 2003, 3:832-844, incorporated herein by reference).
This concept of cancer stem cells further implies that common genetic pathways might define critical stem cell-like functions in neoplastic stem cells, as well as in normal stem cells (Lessard, J. and Sauvageau, G. BMI-1 determines the proliferative capacity of normal and leukaemic stem cells. Nature 2003, 423:255-260; Pardal, R., Clarke, M. F., Morrison, S. J. Applying the principle of stem-cell biology to cancer. Nature Review Cancer 2003, 3:895-902, incorporated herein by reference). In colorectal cancer, for example, constitutive activation of the β-catenin/TCF-4 pathway imposes a crypt progenitor phenotype on colorectal cancer cells, suggesting that analysis of normal stem cells and cancer cells may reveal common stem cell-like pathways engaged in malignant cells (van den Wetering, M., Sancho, E., Verweij, C., et al. The β-catenin/TCF-4 complex imposes a crypt progenitor phenotype on colorectal cancer cells. Cell 2002, 111:241-250, incorporated herein by reference).
Specifically, genes associated with the potential of a stem cell to proliferate are likely to be of particular interest in cancer studies. As one example, recent studies indicate that the Polycomb group (PcG) gene BMI-1 determines the proliferative potential of normal and leukemic stem cells and is required for the self-renewal of hematopoietic and neural stem cells (Lessard, J. and Sauvageau, G. BMI-1 determines the proliferative capacity of normal and leukaemic stem cells. Nature 2003, 423:255-260; Park, I.-K., et al., BMI-1 is required for maintenance of adult self-renewing haematopoietic stem cells. Nature 2003, 423:302-305; Molofsky, A. V., et al., BMI-1 dependence distinguishes neural stem cell self-renewal from progenitor proliferation. Nature 2003, 425:962-967, each incorporated herein by reference). BMI-1 oncogene is expressed in all primary myeloid leukemia and leukemic cell lines that have been analyzed in various studies so far and over-expression of BMI-1 causes neoplastic transformation of lymphocytes (Lessard, J. and Sauvageau, G. BMI-1 determines the proliferative capacity of normal and leukaemic stem cells. Nature 2003, 423:255-260; Lessard, J., et al., Stage-specific expression of polycomb group genes in human bone marrow cells. Blood 1998, 91:1216-1224; Haupt, Y., et al., J. M. BMI-1 transgene induces lymphomas and collaborates with Myc in tumorigenesis. Oncogene 1993, 8:3161-3164; Alkema, M. J., et al., A. Perturbation of B and T cell development and predisposition to lymphomagenesis in Eμ-BMI-1 transgenic mice require the BMI-1 RING finger. Oncogene 1997, 15:899-910, each incorporated herein by reference), Recently, BMI-1 expression was reported in human non-small-cell lung cancer and breast cancer cell lines, suggesting an oncogenic role for BMI-1 activation in epithelial malignancies (Vonlanthen, S., et al. The BMI-1 oncoprotein is differentially expressed in non-small-cell lung cancer and correlates with INK4A-ARF locus expression. Br. J. Cancer 2001, 84:1372-1376; Dimri, G. P., et al., The BMI-1 oncogene induces telomerase activity and immortalizes human mammary epithelial cells. Cancer Res. 2002, 62:4736-4745; LaTulippe, E., et al., Comprehensive gene expression analysis of prostate cancer reveals distinct transcriptional programs associated with metastasis. Cancer Res. 2002, 62:4499-4506, each incorporated herein by reference).
These strong ties between neoplastic stem cells and normal stem cells, and the common genetic pathways defining critical stem cell-like functions in cancer cells, provide a useful opportunity for further analysis. Expression profiling of tumor samples using oligonucleotide or cDNA microarray technology is a powerful tool for revealing multiple gene expression signatures associated with various cancers. For example, comparative gene expression profiling analysis of normal stem cells and cancer cells may reveal gene expression signatures of “stemness” pathways engaged in malignant cells. These gene signatures identified to be associated with certain cancers and identified to have an association with stem cell-like properties could then be used prognostically to predict clinical outcome for a particular patient. Accuracy of different technologies using expression profiling for providing diagnosis and prognosis could be increased through identification of small signatures that are highly effective in providing information regarding likely clinical outcome for a cancer patient, even in the early stages of the cancer. These gene signatures could act as powerful predictors of distant metastasis, short interval to disease recurrence, death after therapy in cancer patients, and so forth, thus providing cancer patients with essential information before the cancer has had a chance to progress.
Thus, there exists in the art a need for improved methods of predicting the clinical outcome of disease states, such as cancer, through use of gene signatures associated with genes that are differentially expressed or regulated in biological samples, such as tumor and normal cell samples. The present invention addresses these and other shortcomings of the art.